Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences

Nucleic Acids Research

Volumn 30, Issue 14, 2002, Pages 3214-3224

  Frith, Martin C ^a   Spouge, John L ^d   Hansen, Ulla ^a,c   Weng, Zhiping ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

^c Boston University   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MUSCLE PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; CIS ISOMER; CONTROLLED STUDY; ENHANCER REGION; EXTRACELLULAR MATRIX; GENE CLUSTER; GENE CONTROL; INTERMETHOD COMPARISON; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MOTIF; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE;

EID: 0037100636     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf438     Document Type: Article

References (71)

1. Initial sequencing and analysis of the human genome
2. From bioinformatics to computational biology
3. The hardwiring of development: Organization and function of genomic regulatory systems
4. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
5. Localization of Xenopus Vg1 mRNA by Vera protein and the endoplasmic reticulum
6. Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats
7. A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter
8. A statistical model for locating regulatory regions in genomic DNA
9. Identification of regulatory regions which confer muscle-specific gene expression
10. Promoter region-based classification of genes
11. Detection of cis-element clusters in higher eukaryotic DNA
12. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
13. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo
14. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes
15. DNA binding sites: Representation and discovery
16. The statistical significance of nucleotide position-weight matrix matches
17. Transcription factor LSF binds two variant bipartite sites within the SV40 late promoter
18. Repression of HIV-1 transcription by a cellular protein
19. Molecular cloning of the alpha-globin transcription factor CP2
20. Activation of RNA polymerase II transcription by the specific DNA-binding protein LSF. Increased rate of binding of the basal promoter factor TFIIB
21. Characterization of the molecularly cloned murine alpha-globin transcription factor CP2
22. A novel LBP-1-mediated restriction of HIV-1 transcription at the level of elongation in vitro
23. Repression of human immunodeficiency virus type 1 through the novel cooperation of human factors YY1 and LSF
24. Transcription factor CP2 is essential for lens-specific expression of the chicken alphaA-crystallin gene
25. Identification and characterization of a critical CP2-binding element in the human interleukin-4 promoter
26. Inhibition of the mammalian transcription factor LSF induces S-phase-dependent apoptosis by downregulating thymidylate synthase expression
27. Specific stimulation of simian virus 40 late transcription in vitro by a cellular factor binding the simian virus 40 21-base-pair repeat promoter element
28. Transcriptional control elements and complex initiation pattern of the TATA-less bidirectional human thymidylate synthase promoter
29. The DNA sequence and comparative analysis of human chromosome 20
30. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
31. Bio Prospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
32. Identification of common molecular subsequences
33. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
34. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
35. Methods for calculating the probabilities of finding patterns in sequences
36. Structure-function studies of ETS transcription factors
37. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
38. TRANSFAC: An integrated system for gene expression regulation
39. CART classification of human 5′ UTR sequences
40. Identification and characterization of the potential promoter regions of 1031 kinds of human genes
41. A greedy algorithm for aligning DNA sequences
42. Tandem repeats finder: A program to analyze DNA sequences
43. DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
44. Activation of the myocyte enhancer factor-2 transcription factor by calcium/calmodulin-dependent protein kinase-stimulated binding of 14-3-3 to histone deacetylase 5
45. 14-3-3tau associates with and activates the MEF2D transcription factor during muscle cell differentiation
46. Identification of multiple proteins that interact with functional regions of the human cardiac alpha-actin promoter
47. Activation of the cardiac alpha-actin promoter depends upon serum response factor,Tinman homologue, Nkx-2.5 and intact serum response elements
48. GATA-4 and serum response factor regulate transcription of the muscle-specific carnitne palmitoyltransferase I beta in rat heart
49. Adenylate kinase phosphotransfer communicates cellular energetic signals to ATP-sensitive potassium channels
50. Adenylate kinase 1 gene deletion disrupts muscle energetic economy despite metabolic rearrangement
51. Compromised energetics in the adenylate kinase AKI gene knockout heart under metabolic stress
52. Cloning and expression of human adenylate kinase 2 isozymes: Differential expression of adenylate kinase 1 and 2 in human muscle tissues
53. Tissue-specific and developmentally regulated expression of the genes encoding adenylate kinase isozymes
54. The eukaryotic promoter database (EPD)
55. Prediction of complete gene structures in human genomic DNA
56. The sequence of the human genome
57. Sp1 and kruppel-like factor family of transcription factors in cell growth regulation and cancer
58. Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA
59. Nuclear hormone receptors and gene expression
60. DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites
61. Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites
62. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
63. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
64. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
65. Genomic sequence comparison of the human and mouse adenosine deaminase gene regions
66. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA
67. Human and rodent DNA sequence comparisons: A mosaic model of genomic evolution
68. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome
69. Human-mouse genome comparisons to locate regulatory sites
70. GenBank